On the "my I.D is better than yours" argument against I.D.

Alien Physics: Scientist Offers Novel Escape Hatch from Intelligent Design

David Klinghoffer

As I've said before, intelligent design can take or leave extraterrestrial life. It doesn't affect the cogency of ID arguments one way or the other. Materialism, on the other hand, must have ETs and the more intelligent and advanced, the better. After all, human life can't be special, therefore something like us must be replicated across the cosmos.

The problem is that the universe offers no hint of objective evidence for ETs. So the race is on to find plausible rationales for why the heck not. Enter Columbia University astrophysicist Caleb Scharf with a novel idea: We can't see advanced otherworldly life because it's so advanced it has encoded itself in the structure of the universe itself ("Is Physical Law an Alien Intelligence?").

Actually it's literally a novel idea since, as he points out at the end of an article for Nautilus, Carl Sagan came up with it in his science fiction classic Contact back in 1985.

[I]f the cosmos holds other life, and if some of that life has evolved beyond our own waypoints of complexity and technology, we should be considering some very extreme possibilities. Today's futurists and believers in a machine "singularity" predict that life and its technological baggage might end up so beyond our ken that we wouldn't even realize we were staring at it. That's quite a claim, yet it would neatly explain why we have yet to see advanced intelligence in the cosmos around us, despite the sheer number of planets it could have arisen on -- the so-called Fermi Paradox.

For example, if machines continue to grow exponentially in speed and sophistication, they will one day be able to decode the staggering complexity of the living world, from its atoms and molecules all the way up to entire planetary biomes. Presumably life doesn't have to be made of atoms and molecules, but could be assembled from any set of building blocks with the requisite complexity. If so, a civilization could then transcribe itself and its entire physical realm into new forms. Indeed, perhaps our universe is one of the new forms into which some other civilization transcribed its world.

These possibilities might seem wholly untestable, because part of the conceit is that sufficiently advanced life will not just be unrecognizable as such, but will blend completely into the fabric of what we've thought of as nature. But viewed through the warped bottom of a beer glass, we can pick out a few cosmic phenomena that -- at crazy as it sounds -- might fit the requirements.

What's that about a beer glass?

Actually, this is clever as a thought experiment. As an illustration of how his alien physics idea might be true, he suggests that mysterious dark matter, thought to constitute 27 percent of the mass and energy of the universe we see, might not be the formless, structure-less stuff we imagine. Perhaps it's more like cloud storage for alien civilizations that have uploaded themselves.

Coming on top of biologist Andy Gardner's proof against ID that I mentioned this morning -- from the fact that gazelles don't leap into the mouths of waiting cheetahs, as a perhaps "slightly facetious" Dr. Gardner would design things if he were in charge -- this is a good day for some rather underwhelming attempts to escape from scientific indications of ID.

So Scharf's escape hatch is to posit alien design in the cosmos in the form of physics and its laws. At first glance this doesn't sound radically at variance with Discovery Institute biologist Michael Denton's argument (see the Privileged Species website) that chemistry and physics, with their extraordinarily detailed fitness for life, give evidence of design.

One difference is that a suggestion like Scharf's is intended, perhaps not consciously, to evade the possibility that a designer is outside nature, something that the game of science as currently played arbitrarily excludes. Denton more reasonably leaves the question open. The other difference is that Denton's evidence is massive, while Scharf's is hard to distinguish from sci-fi.

On the "If I were God" argument against I.D

Biologist's New Argument Against Intelligent Design: Under ID, Gazelle Should Run Toward Cheetah

David Klinghoffer

It will be a treat to have the recording of last week's Royal Society conference, "New Trends in Evolutionary Biology,," to confirm the exact wording of a few choice quotes from the event. We've already pointed out this slide from Andy Gardner   of the University of St. Andrews. It says that Darwinism's "process" is "natural selection," its "purpose" being to "maximize fitness." ID's "process," on the other hand, is "God did it" while its purpose is "???"

What a way to turn a serious argument into a ludicrous cartoon. Completing the picture, Evolution News contributor Jonathan M., who was in the audience, notes on Facebook today that Dr. Gardner added a further observation. We alluded to this briefly before, but it deserves special highlighting. Jonathan writes, "And of course, if God made the gazelle, he would have made it run towards the cheetah. He really said this."

We've now had two reports of this. I double-checked to make sure there was no misunderstanding on my part or humorous intent on Jonathan's.

I am not joking. He said that, if the gazelle was designed, then its "purpose" is to provide food for the cheetah; and so we should expect it to be designed to run towards the cheetah rather than away. I think he was being slightly facetious but he really did say that.
"Slightly facetious" or not, folks, what we have here is a biologist speaking on "Anthropomorphism in evolutionary biology" before the world's most august scientific body and telling those assembled that, if ID is true, the direction of the gazelle's fleet running is in the wrong direction. It ought to jump straight into the cheetah's mouth.


Can you make this stuff up? Maybe you could. For myself, I don't have the imagination for it.

It's irreducible complexity all the way down.

What It Takes to Build a Hook for the Flagellum
Evolution News & Views

You've just been hired as a software engineer. Your first project is to write code that will operate robotic machines. The robots need to build a high-speed universal joint and fasten it to a shaft that will rotate at high speed. The code needs to select materials that can tolerate the high stresses they will face, and arrange them into flexible, mutually-reinforcing configurations that will provide high performance and fault tolerance over many cycles of switching between prograde and anterograde rotations. Oh, and it needs to be hollow so that other materials can pass through during operation. Good luck.

Would everyone agree a new hire facing this challenge had better have high intelligence, combined with a great deal of experience with materials and Einsteinian knowledge of physics? What if you were told the company is considering farming out the task to a brainless entity with no sensors that can only rely on sheer dumb luck?

New light has been shed on just one part of the molecular machine that started Michael Behe on his revolutionary role as a champion of intelligent design: the bacterial flagellum. We often hear the parts of this iconic molecular machine rattled off in a list: rotor, stator, hook, propeller etc. The elegant animations in our new documentary Revolutionary certainly make the point, but not shown are some additional levels of complexity beneath the exterior that put extra oomph into the case for ID. A new paper opens Darwin's black box further.

In Nature Communications, five researchers from the Okinawa Institute of Science and Technology in Japans describe the "complete structure of the bacterial flagellar hook" in Campylobacter jejuni, a bacterium with a single flagellum at one end of its spiral-shaped rod-like cell (some varieties have two flagella, one at each pole). C. jejuni colonizes the digestive tracts of cattle and many birds without apparent harm, but we humans don't want it in our guts, because it is a major cause of food poisoning. Proper cooking of poultry and meat usually prevents disease. But we digress; such matters are beyond the domain of intelligent design theory. The focus is on whether the flagellar hook is designed or not.

Before looking at C. jejuni's flagellum, let's compare the outboard motor styles of different bacteria. The authors write:

Flagella are found in both gram-positive and gram-negative bacteria. Although flagellar hooks appear identical at first sight, the diversity of flagellar hook proteins suggests that the hooks have diverged to specifically fit the motility requirements of each bacterium. The cells of the food-borne pathogen, Campylobacter jejuni (C. jejuni) are spiral-shaped and are able to move using unipolar or bipolar flagella, in comparison with rod-shaped S[almonella] enterica cells, which move using many peritrichous flagella over the cell surface. Uniquely, the C. jejuni flagellar hook is also used to export virulence factors during colonization of the avian or human host. Intriguingly, the C. jejuni hook protein, FlgEcj, has one of the longest amino acid sequences compared with other bacterial FlgE proteins. Compared with FlgE from S. enterica, FlgEcj is about twice as large. We solved the structure of the hook of a fliK null mutant strain derived from C. jejuni strain 81116 (NCTC 11828) by electron cryo-microscopy, using single-particle averaging methods with image segment classification followed by systematic symmetry exploration. [Emphasis added.]
As stated, there appear to be "motility requirements" behind the different motor styles, even though the authors do not question whether they evolved:

Flagella, although macroscopically similar, have evolved features that will make them specially adapted to particular tasks. The intestinal jejunum is a viscous environment where C. jejuni is adapted for swimming. The results shown here tend to support the idea that additional strengthening of the hook in C. jejuni is necessary to enable motility in this viscous environment.
So they are really talking about adaptation, not evolution. Nowhere do they describe how this extra-strong flagellum originated or how it evolved from another species. One story they tell is beside the point:

Amino acid sequence variability in the central parts of FlgE proteins of C. jejuni strains was proposed to occur because of selection pressure during host invasion to generate variations in surface-exposed antigenic determinants. The variable regions do indeed correspond to the surface-exposed region of C. jejuni hook domains D3 and D4. The variability is tolerated because these regions are not essential for intra-molecular contacts that organize the hook.
That appears to be a case of degeneration, not innovation. It's a type of variation not related to function.

What they really know is that this flagellar hook meets the design requirements for its particular environment. The point of their paper is that the hook region of this species' outboard motor, "reveals extensive set of stabilizing interactions."

That's where things get interesting, because a hook is really a universal joint. A universal joint has to be able to transmit rotary power from a shaft through a range of angles. The laws of physics come into play here: torque, angular momentum, and material strain. An outboard motor with a universal joint will have to meet design requirements to handle extra strain, especially when the viscosity of its medium increases. Think of the stresses on a universal joint operating in oil instead of water, for instance. Now rev up the RPMs, and you can see what the software engineer is up against!

Bacterial flagella have long been studied, but many aspects of their structure and function are still eluding us. The structure of the hook can be described as a tubular helical structure. The hook functions like a universal joint. It transmits the torque, produced by the motor located in the cell membrane, to the filament that acts like a propeller. The assembly of about a 100 copies of a single protein, FlgE, makes the bacterial flagellar hook. An exported molecular ruler protein, FliK, controls the hook length. Cells bearing mutations in the fliK gene produce abnormally long 'polyhook' structures. The bacterial flagellar motor rotates at frequencies that vary between 100 Hz and 2,000 Hz depending on bacterial species. The hook undergoes multiple conformational changes while rotating around its axis. During these conformational changes, the interactions between the FlgE molecules must secure the stability while enabling the dynamic nature of the hook.
Get that calculator out. 100 Hz is 6,000 RPM; 2,000 Hz is, let's see, yikes! 120,000 revolutions per minute! Our software engineer is getting really worried. His application only has one shaft, but the universal joint has to handle extreme torque in viscous fluid. The strain on the material is going to be enormous! How can he make it strong enough without compromising its flexibility?

Extra domains in FlgE, found only in Campylobacter and in related bacteria, bring more stability and robustness to the hook. Functional experiments suggest that Campylobacter requires an unusually strong hook to swim without its flagella being torn off.
If the engineer is smart, he will just mimic the elegant solution of the bacterium C. jejuni. Take a look at Figure 2 in the open-access paper. It's beautiful. Multiple strands of the FlgE protein (remember, it's twice as long as its counterparts in other species) intertwine in five layers. Each layer contains complex interactions with the other layers, providing the strength needed for the application, "while still allowing it to curve." Even more amazing, "the interactions between the molecules that make the hook are transient interactions where interacting amino acid residues will constantly change partners during the rotation of the hook."

A committed Darwinist might still be able to weave a just-so story about how this hook evolved. Once upon a time, Campylobacter having a simpler hook with fewer strands of FlgE invaded a new environment that was more viscous. By accident, a mutant with duplicate layers of FlgE succeeded in swimming without its flagella being torn off, so its descendents survived. By another accident, the ones with longer FlgE proteins also survived, perhaps by duplication. Somehow, blindly, complex transient interactions arose... etc. Sound convincing?

Evolutionists might argue that the hook only employs FlgE proteins, so it is not irreducibly complex. Nothing about Behe's irreducible complexity principle, however, requires multiple types of materials. It's their arrangement for function that matters. All the parts for a mousetrap, for instance, could be made of iron. In the case of the flagellar hook, the arrangement of the proteins in multiple layers with multiple transient interactions is the key to its operation. Remove these layers and interactions, and the flagellum would be torn off when the bacterium tried to swim.

We haven't even addressed the issue of how this hook is assembled in the cell. To be heritable, mutations would have had to occur in the DNA. Those mistakes would have to evade the proofreading mechanisms of the cell during transcription and translation. But even if the mutant proteins arrived at the construction site (at the right time and in the right quantities, don't forget), how would other molecular machines know what to do with them? Unless they got assembled correctly so that the transient interactions would take place properly during operation, they would provide no benefit; there would be no "selection pressure" to maintain them. The evolutionary story seems even more implausible at the level of coding and construction.


So there you have it: even the hook of the famous flagellum is irreducibly complex. It is amazingly well designed for its task within a task, that of being an essential part of a multi-part molecular machine. As Jonathan Wells says, "What we have here is irreducible complexity all the way down."

Doing well by doing good.

Witnesses Win Major Awards for Green Building Design and Construction

NEW YORK—Jehovah’s Witnesses, well-known for their global Bible education work, are receiving recognition for excellence in environmentally sustainable building design and construction.



The Green Building Initiative (GBI) awarded certifications for two new buildings at the Witnesses’ United States branch facilities in Wallkill, New York: the Watchtower Farms F Residence, completed in late 2012, and the Watchtower Wallkill Office Building, completed in 2014. Both of the buildings received the highest award of Four Green Globes.


Watchtower Wallkill Office Building


Shaina Sullivan, Marketing Director for GBI, notes: “Worldwide, less than 4 percent of all buildings assessed under the program have achieved this top certification of Four Green Globes.” Ms. Sullivan added that the Watchtower Wallkill Office Building “is the first nonresidential project in New York State to earn this rating.” Jenna Middaugh, Project Manager for GBI, commented: “Of the 23 buildings [in the United States] that have been certified with Four Green
 Globes since 2006, the Watchtower Wallkill Office Building achieved the highest point score with 94 percent.”


Watchtower Farms F Residence

GBI administers Green Globes as a commercial rating system and certification program that utilizes a third-party on-site assessment of sustainable design and construction. Achieving a Green Globes rating requires environmentally sensitive site design that focuses on water management, minimization of energy consumption and greenhouse gas emissions, minimizing the impact on natural resources by selection of appropriate materials, and creating a healthful indoor environment.


Photovoltaic panels provide at least 10 percent of the electrical energy needs for the Watchtower Wallkill Office Building, a feature of the building’s award-winning sustainable design.

David Bean, sustainable design coordinator for the Witnesses’ facilities in the United States, says: “The achievement of these awards attests to the high standard of design and construction work that we set for all of our projects. We are also pursuing Green Globes certification in the design and construction of our new world headquarters in Warwick, New York.”


Installation of a green roof, one of the sustainable features of the Witnesses’ new world headquarters in Warwick, New York.

Zeny St. Jean, who coordinates global building projects for Jehovah’s Witnesses from their world headquarters, states: “While our primary focus is the advancement of Bible education, we appreciate these awards as professional recognition of the environmentally conscientious building design and construction that we strive to implement at our facilities around the world.”

Media Contact(s):


International: J. R. Brown, Office of Public Information, tel. +1 718 560 5000

Phone call for Dr.Moreau!

"The Link," or Science Fiction Double Feature: Dr. X Builds a Creature...
Richard Sternberg 

(Cue music.) Or, rather, a lemur. Almost every TV channel it seems ran a commercial announcing a documentary about the fossil find of the century, The Link, which will be encored on the History Channel tonight. "Ida," as the female holotype of Darwinius masillae has been playfully dubbed, is the prehistoric prosimian that is the focus of attention. The story of her discovery is the stuff of every good science-fiction B-movie from the 1950s : A "secret study" conducted by an "international team of scientists," has led to earth-shattering results that can only now be revealed to the world. Think Creature from the Black Lagoon (because of the fossil find) meets When Worlds Collide (because of the impact that will be felt on your everyday life) and you'll be close to the stated importance of the program. All that's missing are some Tesla coils, a hidden lair in a dead volcano, the fallout from an atomic explosion, and a UFO landing on the National Mall. Presumably such extra features, along with more specifics about the significance of her all too brief life -- "a child when she died, but she'll change history forever" -- can be gathered from the just-released book, The Link.

It's just a jump to the left...

Of the cladogram, I mean. There is one clade of primates called the Strepsirrhini ("wet noses") that includes the lemurs, the dwarf and mouse-lemurs, the Aye-aye, the lorisids, and the galagos. Ida falls within this suborder according to one hypothesis.

With your hands on your hips...

You will kindly note the other clade of primates termed the Haplorrhini, the sister group of the strepsirrhines. This taxon of the "dry noses" contains the apes, monkeys, and tarsiers. An alternative phylogenetic hypothesis would place Darwinius at the base of this assemblage.

All the brouhaha thus boils down to whether Ida had a wet nose or a dry nose that -- given her status as a transitional form -- was occasionally runny. The theme of The Link is that the latter is a sure bet. For myself, regarding these two alternative evolutionary scenarios, I say...Let's do the Time Warp again...

Anyhow, there I sat yesterday evening, with voyeuristic intention no less, my gin and tonic prepared and my lit cigarette firmly affixed in its black holder, shivering with antici......pation. For, indeed, I wanted to go up to the lab in order to see what's on that slab. But it wasn't the rain that was to blame for my later symptoms of underwhelment. No. It was that after all the commercial hoopla, I expected to hear a speech close to that given by the indefatigable Dr. Furter (Tim Curry) just prior to the dramatic vivification of his creature. That is, my expectation was to see and listen to a pronouncement much like this:

Tonight my conventional unconventionalists, you are to witness a new breakthrough in phylogenetic research and career paradise...is to be mine!

It was strange the way it happened. Suddenly you get a break...All the pieces seem to fit into place. What a sucker you've been...what a fool. The answer was there all the time [on the fossil market, that is]. It took a small accident to find it...an accident! And that's how I discovered the secret, that elusive ingredient, that spark...that is The Link. Yes. I have that knowledge. I hold the secret...to evolution itself!

My interest of course did not concern who actually said it. Or that he would be wearing a tee shirt and jeans as opposed to a green surgical smock over a corset and fishnets (and adorned with oversized pearls). Not at all. What I instead wanted to view was a program where the could-be's and perhapses, the equivocations and qualifications, the oh so many "well, on the one hand...but, then again, on the other" semantic hedges, that are de rigueur in documentaries about evolution, had been dropped with an unabashed flair.

Is it not The Link? Does it not change everything? I asked.

Obviously, as no doubt anyone of you could have told me, my expectations were misplaced. Part of me also desired to see an animation of Ida throw a bone into the air and then have the scene immediately segue to that of a futuristic Pan Am spacejet on its way to an orbiting station called "Darwin 9000," set to the opening strains of Johann Strauss II's "On the Beautiful Blue Danube." I was mentally blending genres in my hopes, true, but in my defense the commercial had promised so very much.

Alas, the disappointment that soon arose in me after the documentary stemmed from the vagueness of it all...that The Link is actually a kind of, sort of, nth cousin mth removed of the side lineage that some hypothesize possibly gave rise to the distant ancestors of what quite conceivably became the hominid branch of the Darwinian tree. And to think that I could have been watching reruns of Mystery Science Theatre 3000 or the cult classic, The Phantom of the Paradise.

To be certain, the authors of the PLoS One paper were appropriately circumspect in their paper, so one should not misconstrue my peeve as really being about the finer details of basal primate taxonomy. As far as I'm concerned, Ida may well be the transitional taxon linking the Strepsirrhini and Haplorrhini. Fine. Who is going to get strung out -- to again borrow a phrase from the illustrious Dr. Furter -- if the Notharctidae and Cercamoniinae are rendered by implication paraphyletic, wastebasket taxonomic groupings? Who? Nor is there a limit to such theoretical gratuity...should someone even want to posit that each and every genus in the Cercamoniinae, from Anchomomys to Darwinius to Pronycticebus, is in its own right a missing link -- the same way, you know, that everyone's special -- no complaint will be uttered from this quarter. Not so much as a peep.

Irksome, though, was the way in which an old story was sold as something profoundly novel. While watching it, I could almost hear the creator of this work of science fiction (defined by that definitive fount of knowledge Wikipedia as "science-based depictions of phenomena that aren't necessarily accepted by mainstream science," emphases mine) singing as the fossil was presented: In just seven days...I can make you a humaaaannnnnn. (My sincerest apologies to Richard O'Brien of the Rocky Horror Picture ShowR for the way I have twisted his lines and songs from the film.) But the issue is that a familiar feeling emerged while watching the piece, the one we have all had in the theater. It arises the moment you realize that you know the plot, the narrative. The only difference is that the characters and the actors playing them have changed, along with the music and the CGI effects. Eight years ago it was the Urwhale. Last year it was the Ursalamander. Last night it was the Urmonkey. Still, the same story...

That said, I would not have been so underwhelmed had someone just blurted out in the first few minutes -- like the inimitable Charles Gray does at the end of Rocky Horror -- the central theme of the documentary, that "crawling...on the planet's face...some insects called the human race. Lost in time...lost in space...and meaning."


R(Rated R) -- For mature audiences only.

On the grandfather of I.D.

Michael Behe on the Legacy of Denton's Evolution: A Theory in Crisis
David Klinghoffer









Ever wonder what major and highly original scientific advocates of intelligent design think of each other's work? In a brief video conversation, Michael Behe comments on the impact and significance of Michael Denton's books Evolution: A Theory in Crisis  and Evolution: Still a Theory in Crisis , culminating in the typological understanding of life's structures and the fundamental challenge to Darwinian theory that poses.


Dr. Behe's case for ID, first advanced in Darwin's Black Box twenty years ago, is the subject of the new hour-long documentary  Revolutionary: Michael Behe and the Mystery of Molecular Machines, written and directed by John West. Get your copy of Revolutionary, on DVD or Blu-ray, today.

Rich gene,poor gene?

Prince or Pauper? Researchers Find Functional Pseudogene in Fruit Fly
Evolution News & Views 

Suppose we introduced you to a friend and said he works as a pseudoscientist. You would be immediately suspicious of his white lab coat and apparent command of scientific language in subsequent conversation. After all, he just pretends to be a scientist. He's fake. He's false. He is bogus, sham, phony, mock, ersatz, quasi-, spurious, deceptive, misleading, assumed, contrived, affected, insincere, and all the other negative synonyms we associate with the prefix pseudo.

But then suppose we corrected the description and said that, actually, he is a "pseudo-pseudoscientist." The double negative suddenly opens the possibility that he really is a scientist. He's faking his fakery, contriving his contrivance, mocking insincerity for some reason. Maybe he's a psychologist studying the effects of perceived pretentiousness, using you as his lab rat. Maybe he's a real MD playing a doctor on a fictional TV show, leading us to believe he is "just an actor." Think of the guards in Mark Twain's The Prince and the Pauper who quickly escort the shabbily dressed prince off the palace grounds without noticing the royal seal in his pocket. Have scientists too quickly dismissed pseudogenes as broken genes, worthless transcripts of DNA without function? Could at least some of them be "pseudo-pseudogenes"?

A surprising paper in Nature actually uses that term: "Olfactory receptor pseudo-pseudogenes." Researchers in Switzerland found a case in a species of fruit fly that defies the pseudogene paradigm. Pseudogenes are often suspected of being broken genes when a premature termination codon (PTC) is found in the DNA sequence. Obviously, such a gene could not be translated into a functional protein, right? Translation would stop before the messenger RNA is complete. Often, that is the case. What good is that?

These scientists found something interesting about an olfactory receptor gene in Drosophila sechellia, "an insect endemic to the Seychelles that feeds almost exclusively on the ripe fruit of Morinda citrifolia." They looked at its Ir75a locus, a gene that encodes an olfactory receptor for acetic acid in its more famous cousin D. melanogaster, Finding a PTC in this species' Ir75a gene, they initially thought it was a broken gene -- a pseudogene. The abstract begins with the usual evolutionary rhetoric about pseudogenes:

Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes. Although certain pseudogene-derived RNAs have regulatory roles, and some pseudogene fragments are translated, no clear functions for pseudogene-derived proteins are known. Olfactory receptor families contain many pseudogenes, which reflect low selection pressures on loci no longer relevant to the fitness of a species. [Emphasis added.]
That's their setup for the surprise announcement. This pseudogene might just be a "pseudo-pseudogene"! It might be a prince masquerading as a pauper.

What started them on their paradigm-breaking find was noticing that this apparent pseudogene is fixed in the population, suggesting it has a function. Taking a closer look, they found that the translation machinery is able to "read through" the premature stop codon, the PTC. How? They're not sure, but they found something else interesting: the read-though operation works efficiently only in neurons, not other types of cells. That opens up a whole new way of looking at pseudogenes: some of them might be tissue-specific regulators.

It is not yet clear how the D. sechellia Ir75a PTC is read through. It cannot be because of insertion of the alternative amino acid selenocysteine (which is incorporated at UGA18). Moreover, no suppressor tRNAs are known in D. melanogaster and ribosomal frame-shifting is also unlikely because there is no change in the reading frame after the PTC. We suggest that read-through is due to PTC recognition by a near-cognate tRNA that allows insertion of an amino acid instead of translation termination. Although the trans-acting factors regulating read-through are unclear, the neuronal specificity of this process is reminiscent of RNA editing and micro-exon splicing, in which key responsible regulatory proteins are neuronally enriched. We therefore speculate that tissue-specific expression differences in tRNA populations underlie neuron-specific read-through.
We might be tempted to dismiss this as a rare case of evolutionary tinkering. The gene broke, but natural selection found a way to tinker with it and get it to work. Perhaps. But further experimentation with D. melanogaster suggests that "pseudogenization" has a logical function: it works to tune odor sensitivity. The part of the gene downstream from the PTC apparently affects the type of receptor produced. What's more, this kind of regulation might not be rare.

Read-through is detected only in neurons and is independent of the type of termination codon, but depends on the sequence downstream of the PTC. Furthermore, although the intact Drosophila melanogaster Ir75a orthologue detects acetic acid -- a chemical cue important for locating fermenting food found only at trace levels in Morinda fruit -- D. sechellia Ir75a has evolved distinct odour-tuning properties through amino-acid changes in its ligand-binding domain. We identify functional PTC-containing loci within different olfactory receptor repertoires and species, suggesting that such 'pseudo-pseudogenes' could represent a widespread phenomenon.
Experiments showed that the Ir75a 'pseudo-pseudogene' actually yields a functional odor receptor, but not for acetic acid as in D. melanogaster. Instead, it makes a receptor tuned for similar acidic odorants unique to food sources available on the Seychelles. The tissue-specific read-through capabilities of this gene provide the fly with a way to detect food sources it needs in its environment.

Perhaps nothing beyond chance mutation or neutral drift is needed to explain this. On the other hand, the research team may have stumbled onto an important function for pseudogenes.

Our efforts to understand the molecular basis of the loss of olfactory sensitivity to acetic acid in D. sechellia led us to discover a notable and, to our knowledge, unprecedented evolutionary trajectory of a presumed pseudogene. Efficient read-through of a PTC in D. sechellia Ir75a permits production of a full-length receptor protein, in which reduction in acetic acid sensitivity and gain of responses to other acids is due to lineage-specific amino acid substitutions in the LBD pocket. The PTC does not noticeably influence the activity of D. sechellia Ir75a, suggesting that it is selectively neutral from an evolutionary standpoint. We propose that it became fixed through genetic drift, given D. sechellia's persistent low effective population size.
They can call it an "evolutionary trajectory" if they wish. Another way of looking at this is a design feature. The premature stop codon, or PTC, may be more elegant than a stop sign. It may be a switch, telling the translation machinery to pay attention to the downstream code if -- and only if -- translation is taking place inside neuronal cell. In non-neuronal cells, the PTC might indeed say "stop," delivering the transcript to the trash. In neurons, though, environmental cues may trigger pre-existing routines to fine-tune the sensitivity to odorants available in food sources.

A design perspective could accelerate discoveries along this line. We've seen the tendency to dismiss things as evolutionary castoffs when their functions were not understood, only to find higher levels of organization at work. Introns are spliced out of messenger RNAs; they must be junk. Methyl groups interfere with translation; they must be mistakes. Retrotransposons must be parasites. Pseudogenes must be broken genes. Maybe not. If scientists had expected design, maybe they would have hit upon today's paradigms about epigenetics, alternative splicing and gene regulation sooner.


Intelligent design theory doesn't require everything to be designed. It does, however, prevent a "premature stop" to dismissing things as not designed.

The Watchtower society's commentary on the"Altar"

ALTAR

Basically, a raised structure or place on which sacrifices are offered or incense is burned in worship of the true God or of another deity. The Hebrew word miz·beʹach (altar) comes from the root verb za·vachʹ (slaughter; sacrifice) and thus basically refers to a place of slaughtering or sacrificing. (Ge 8:20; De 12:21; 16:2) Similarly, the Greek thy·si·a·steʹri·on (altar) comes from the root verb thyʹo, also meaning “slaughter; sacrifice.” (Mt 22:4; Mr 14:12) The Greek word bo·mosʹ refers to the altar of a false god.—Ac 17:23.

The first mention of an altar occurs after the Flood when “Noah began to build an altar to Jehovah” and offered burnt offerings thereon. (Ge 8:20) The only offerings mentioned prior to the Flood were those of Cain and Abel, and though it is likely that they did so, it is not stated whether they used altars or not.—Ge 4:3, 4.

Abraham built an altar at Shechem (Ge 12:7), at a point between Bethel and Ai (Ge 12:8; 13:3), at Hebron (Ge 13:18), and also evidently on Mount Moriah, where he sacrificed a ram given him by God in substitution for Isaac. (Ge 22:9-13) Only in this last case is a sacrifice specifically mentioned as being offered on these altars by Abraham. However, the basic meaning of the Hebrew word indicates that offerings were likely made in each case. Isaac later built an altar at Beer-sheba (Ge 26:23, 25), and Jacob built altars at Shechem and at Bethel. (Ge 33:18, 20; 35:1, 3, 7) These altars made by the patriarchs were doubtless of the type later mentioned by God in the Law covenant, either mounds of earth or platforms consisting of natural (unhewn) stones.—Ex 20:24, 25.

Moses constructed an altar following the victory over Amalek, naming it Jehovah-nissi (Jehovah Is My Signal Pole). (Ex 17:15, 16) At the making of the Law covenant with Israel, an altar was built by Moses at the foot of Mount Sinai, and sacrifices were offered up on it. Blood from the sacrifices was sprinkled on the altar, on the book, and on the people, thereby validating and putting in force the covenant.—Ex 24:4-8; Heb 9:17-20.

Tabernacle Altars. With the setting up of the tabernacle, two altars were constructed according to divine pattern. The altar of burnt offering (also called “the altar of copper” [Ex 39:39]) was made of acacia wood in the form of a hollow chest, apparently without top or bottom. It was 2.2 m (7.3 ft) square and 1.3 m (4.4 ft) high with “horns” projecting from the upper four corners. All its surfaces were overlaid with copper. A grating, or network, of copper was placed below the altar’s rim “down within,” “toward the center.” Four rings were placed at the four extremities near the grating, and these appear to be the same rings through which the two copper-sheathed acacia-wood poles were passed for carrying the altar. This might mean that a slot was cut through two sides of the altar allowing for a flat grating to be inserted, with the rings extending out on both sides. There is considerable difference of opinion among scholars on the subject, and many consider it likely that two sets of rings were involved, the second set, for insertion of the carrying poles, being attached directly to the outside of the altar. Copper equipment was made in the form of cans and shovels for the ashes, bowls for catching the blood of the animals, forks for handling the flesh, and fire holders.—Ex 27:1-8; 38:1-7, 30; Nu 4:14.

This copper altar for burnt offerings was placed before the entrance of the tabernacle. (Ex 40:6, 29) While it was of relatively low height, thus not necessarily requiring a means of approach, for ease of handling the sacrifices placed within it the earth may have been raised around it or there may have been a ramp leading up to it. (Compare Le 9:22, which states that Aaron “came down” from making offerings.) Since the animal was sacrificed “at the side of the altar to the north” (Le 1:11), “the place for the fatty ashes” removed from the altar was to the E (Le 1:16), and the basin of copper for washing was located to the W (Ex 30:18), this would logically leave the S as the open side on which such a means of approach might be placed.

Altar of incense. The altar of incense (also called “the altar of gold” [Ex 39:38]) was likewise made of acacia wood, the top and sides being overlaid with gold. A border of gold ran around the top. The altar measured 44.5 cm (17.5 in.) square and 89 cm (2.9 ft) high, and also had “horns” extending out from the four top corners. Two gold rings were made for the insertion of the carrying poles made of acacia overlaid with gold, and these rings were placed underneath the gold border on opposite sides of the altar. (Ex 30:1-5; 37:25-28) A special incense was burned on this altar twice daily, in the morning and in the evening. (Ex 30:7-9, 34-38) The use of a censer, or a fire holder, is elsewhere mentioned for burning incense, and evidently such was employed also in connection with the altar of incense. (Le 16:12, 13; Heb 9:4; Re 8:5; compare 2Ch 26:16, 19.) The position of the altar of incense was within the tabernacle just before the curtain of the Most Holy so that it is spoken of as being “before the ark of the testimony.”—Ex 30:1, 6; 40:5, 26, 27.

Sanctification and use of tabernacle altars. At the time of the installation ceremonies, both altars were anointed and sanctified. (Ex 40:9, 10) At that time, as also in subsequent sacrifices of certain sin offerings, blood of the sacrificed animal was put upon the horns of the altar of burnt offering, and the rest was poured out at its base. (Ex 29:12; Le 8:15; 9:8, 9) Some of the anointing oil and blood on the altar was spattered upon Aaron and his sons and their garments to sanctify them toward the conclusion of the installation ceremony. (Le 8:30) In all, seven days were required for the sanctification of the altar of burnt offering. (Ex 29:37) In other burnt offerings, communion sacrifices, and guilt offerings, the blood was sprinkled about upon the altar, while the blood of fowls sacrificed was spattered or drained at the side of the altar. (Le 1:5-17; 3:2-5; 5:7-9; 7:2) Grain offerings were made to smoke upon the altar as “a restful odor” to Jehovah. (Le 2:2-12) Remaining portions of the grain offering were eaten by the high priest and his sons alongside the altar. (Le 10:12) Annually on Atonement Day the altar was cleansed and sanctified by the high priest’s placing some of the sacrificial animals’ blood on the horns of the altar and by spattering it seven times upon the altar.—Le 16:18, 19.

In all the animal sacrifices presented, portions of the animal were made to smoke upon the altar, and for this purpose a fire was maintained on the altar and was never allowed to go out. (Le 6:9-13) From here the fire was obtained for the burning of incense. (Nu 16:46) Only Aaron and those of his descendants who were free from defects were permitted to serve at the altar. (Le 21:21-23) The other Levites were only assistants. Any man not of the seed of Aaron drawing near was to be put to death. (Nu 16:40; 18:1-7) Korah and his assembly were destroyed for failing to recognize this divine assignment, and the copper fire holders that they had taken were made into thin metal plates and overlaid on the altar as a sign that no one not of the offspring of Aaron should draw near.—Nu 16:1-11, 16-18, 36-40.

Once a year the golden altar of incense was also atoned for by the placing of sacrificial blood upon its horns. Other occasions on which it was so treated were when the sin offerings were made for members of the priesthood.—Ex 30:10; Le 4:7.

When being transported by the sons of Kohath both the altar of incense and the altar of burnt offerings were covered, the first with a blue cloth and sealskins, the second with a reddish-purple wool cloth and sealskins.—Nu 4:11-14; see TABERNACLE.

Temple Altars. Prior to the dedication of Solomon’s temple, the copper altar made in the wilderness served for Israel’s sacrificial offerings at the high place in Gibeon. (1Ki 3:4; 1Ch 16:39, 40; 21:29, 30; 2Ch 1:3-6) The copper altar thereafter made for the temple covered an area 16 times as large as the one made for the tabernacle, measuring about 8.9 m (29.2 ft) square and about 4.5 m (14.6 ft) high. (2Ch 4:1) In view of its height, some means of approach was essential. God’s law prohibited the use of steps to the altar to prevent exposure of nakedness. (Ex 20:26) Some believe that the linen drawers worn by Aaron and his sons served to obviate this command and thus made steps allowable. (Ex 28:42, 43) However, it seems likely that an inclined ramp was used to approach the top of the altar of burnt offering. Josephus (The Jewish War, V, 225 [v, 6]) indicates that such an approach was used for the temple altar later built by Herod. If the arrangement of the altar of the temple followed that of the tabernacle, the ramp was probably on the S side of the altar. “The molten sea,” where the priests washed, would thus be convenient, as it also lay toward the south. (2Ch 4:2-5, 9, 10) In other respects the altar constructed for the temple apparently was modeled after that of the tabernacle, and no detailed description of it is given.

It was located where David had earlier built his temporary altar on Mount Moriah. (2Sa 24:21, 25; 1Ch 21:26; 2Ch 8:12; 15:8) This is also traditionally held to have been the location where Abraham had attempted to offer up Isaac. (Ge 22:2) The blood of sacrificial animals was poured out at the altar’s base, and it is likely that some kind of conduit existed for carrying the blood away from the temple area. Herod’s temple is reported to have had such a conduit connected with the SW horn of the altar, and in the rock of the temple area, an opening has been found that leads to an underground channel going out to the Kidron Valley.

The altar of incense for the temple was made of cedarwood, but this seems to have been the only difference between it and that of the tabernacle. It was likewise overlaid with gold.—1Ki 6:20, 22; 7:48; 1Ch 28:18; 2Ch 4:19.

At the inauguration of the temple Solomon’s prayer was offered before the altar of burnt offering, and at its conclusion fire came down from the heavens and consumed the sacrifices on the altar. (2Ch 6:12, 13; 7:1-3) Despite the fact that it covered an area of over 79 sq m (850 sq ft), this copper altar proved too small for the immense quantity of sacrifices made then, and so a portion of the courtyard was sanctified for that purpose.—1Ki 8:62-64.

In the latter part of Solomon’s reign, and in the reigns of Rehoboam and Abijam, the altar of burnt offerings came into neglect so that King Asa found it necessary to renew it. (2Ch 15:8) King Uzziah was stricken with leprosy for attempting to burn incense on the golden altar of incense. (2Ch 26:16-19) King Ahaz moved the copper altar of burnt offering to one side and put a pagan altar in its place. (2Ki 16:14) His son Hezekiah, however, had the copper altar and its utensils cleansed, sanctified, and restored to service.—2Ch 29:18-24, 27; see TEMPLE.

Postexilic Altars. The first thing built in Jerusalem by the returning exiles under Zerubbabel and High Priest Jeshua was the altar for burnt offerings. (Ezr 3:2-6) In due time a new altar of incense was also made.

The Syrian king Antiochus Epiphanes carried off the golden altar of incense, and two years later (168 B.C.E.) he built an altar over the great altar of Jehovah and offered up a sacrifice to Zeus thereon. (1 Maccabees 1:20-64) Judas Maccabaeus thereafter built a new altar of unhewn stones and also restored the altar of incense.—1 Maccabees 4:44-49.

The altar of burnt offerings of Herod’s temple was made of unhewn stones and, according to Josephus (The Jewish War, V, 225 [v, 6]), was 50 cubits square and 15 cubits high, though the Jewish Mishnah (Middot 3:1) gives smaller dimensions for it. It was to this altar, therefore, that Jesus made reference in his day. (Mt 5:23, 24; 23:18-20) The altar of incense of that temple is not described, but Luke 1:11 shows that an angel was standing to the right of it when he appeared to John’s father Zechariah.

Altar of Ezekiel’s Temple. In the visionary temple seen by Ezekiel, the altar for burnt offerings was similarly positioned before the temple (Eze 40:47), but it had a different design from that of the previous altars. The altar consisted of several sections successively indented or recessed. Its dimensions are given in measurements of the long cubit (51.8 cm; 20.4 in.). The base of the altar was one cubit thick and had a “lip” of one span (perhaps 26 cm; 10 in.) as a border around the top, thus forming a sort of gutter or channel, perhaps for receiving blood poured out. (Eze 43:13, 14) Resting on the base itself, but set in one cubit from its outer edge, was another section, and it measured two cubits (c. 104 cm; 41 in.) in height. A third section was stepped in one cubit and was four cubits (c. 207 cm; 82 in.) in height. It also had a border surrounding it of a half cubit (c. 26 cm; 10 in.), perhaps forming a second channel or a protective ledge. Finally, the altar hearth extended up yet another four cubits and was also stepped in one cubit from the preceding section; out from it extended four “horns.” Stairs from the E provided approach to the altar hearth. (Eze 43:14-17) As with the altar built in the wilderness, a seven-day period of atonement and installation was to be observed. (Eze 43:19-26) Annual atonement was to be made for the altar along with the rest of the sanctuary on the first day of Nisan. (Eze 45:18, 19) The river of healing waters seen by Ezekiel flowed eastward from the temple and passed S of the altar.—Eze 47:1.

The altar of incense is not mentioned by name in the vision. However, the description of “the wooden altar” at Ezekiel 41:22, particularly the reference to it as “the table that is before Jehovah,” indicates that this corresponded to the altar of incense rather than to the table of showbread. (Compare Ex 30:6, 8; 40:5; Re 8:3.) This altar was three cubits (c. 155 cm; 61 in.) high and evidently two cubits (c. 104 cm; 41 in.) square.

Other Altars. Since the post-Flood population did not continue with Noah in pure worship, it follows that many altars for false worship were produced, and excavations in Canaan, Mesopotamia, and other sites indicate that these existed from the earliest periods. Balaam had seven altars erected successively at three different sites in his vain attempts at calling down a curse on Israel.—Nu 22:40, 41; 23:4, 14, 29, 30.

The Israelites were instructed to tear down all pagan altars and destroy the sacred pillars and poles customarily built alongside them. (Ex 34:13; De 7:5, 6; 12:1-3) They were never to imitate these nor offer up their children by fire as did the Canaanites. (De 12:30, 31; 16:21) Instead of a multiplicity of altars, Israel was to have just one altar for the worship of the one true God, and this would be located at the place Jehovah would choose. (De 12:2-6, 13, 14, 27; contrast this with Babylon, where there were 180 altars to the goddess Ishtar alone.) They were at first instructed to make an altar of unhewn stones following the crossing of the Jordan River (De 27:4-8), and this was built by Joshua on Mount Ebal. (Jos 8:30-32) Following the division of the conquered land, the tribes of Reuben and Gad and the half tribe of Manasseh built a conspicuous altar by the Jordan, which provoked a temporary crisis among the other tribes until it was determined that the altar was no sign of apostasy but only a memorial of faithfulness to Jehovah as the true God.—Jos 22:10-34.

Other altars were constructed, but these appear to have been built for specific occasions, not for continual use, and they were usually built in connection with angelic appearances or at angelic instruction. The one at Bochim and those of Gideon and Manoah were such. (Jg 2:1-5; 6:24-32; 13:15-23) The record concerning the altar set up at Bethel by the people when considering how to prevent the disappearance of the tribe of Benjamin does not indicate whether such had divine approval or was simply a case of their ‘doing what was right in their own eyes.’ (Jg 21:4, 25) As God’s representative, Samuel offered sacrifice at Mizpah and also built an altar at Ramah. (1Sa 7:5, 9, 10, 17) This may have been due to the fact that Jehovah’s presence was no longer in evidence at the tabernacle in Shiloh, following the removal of the Ark.—1Sa 4:4, 11; 6:19-21; 7:1, 2; compare Ps 78:59-64.

Use of temporary altars. On a number of occasions temporary altars were constructed. For example, Saul offered sacrifice at Gilgal and built an altar at Aijalon. (1Sa 13:7-12; 14:33-35) In the first case he was condemned for not waiting for Samuel to do the sacrificing, but the propriety of the locations as places for sacrificing was not considered.

David instructed Jonathan to explain his absence at Saul’s table on the day of the new moon by saying that David was attending an annual family sacrifice at Bethlehem; however, since this was a subterfuge, it cannot definitely be known whether such was really celebrated. (1Sa 20:6, 28, 29) Later, as king, David built an altar on the threshing floor of Araunah (Ornan), and this was at divine command. (2Sa 24:18-25; 1Ch 21:18-26; 22:1) The statement at 1 Kings 9:25 with regard to Solomon’s ‘offering up sacrifices on the altar’ clearly refers to his causing such to be done through the authorized priesthood.—Compare 2Ch 8:12-15.

With the setting up of the temple at Jerusalem, it appears that the altar was now definitely at “the place that Jehovah your God will choose . . . and there you must come.” (De 12:5) Aside from the altar used by Elijah on Mount Carmel in the fire test with the Baal priests (1Ki 18:26-35), only apostasy now caused the setting up of other altars. Solomon himself was the first to be guilty of such apostasy, because of the influence of his foreign wives. (1Ki 11:3-8) Jeroboam of the newly formed northern kingdom endeavored to divert his subjects from going to the temple in Jerusalem by setting up altars at Bethel and Dan. (1Ki 12:28-33) A prophet then foretold that in the reign of King Josiah of Judah priests officiating at the altar in Bethel would be slaughtered and that the bones of dead men would be burned on the altar. The altar was ripped apart as a sign, and the prophecy was later completely fulfilled.—1Ki 13:1-5; 2Ki 23:15-20; compare Am 3:14.

During King Ahab’s rule in Israel, pagan altars flourished. (1Ki 16:31-33) In the time of King Ahaz of Judah, there were altars “at every corner in Jerusalem,” as well as many “high places.” (2Ch 28:24, 25) Manasseh went so far as to build altars within the house of Jehovah and altars for worshiping “the army of the heavens” in the temple courtyard.—2Ki 21:3-5.

Though faithful kings periodically destroyed these idolatrous altars (2Ki 11:18; 23:12, 20; 2Ch 14:3; 30:14; 31:1; 34:4-7), prior to Jerusalem’s fall Jeremiah could still say: “Your gods have become as many as your cities, O Judah; and as many altars as the streets of Jerusalem you people have placed for the shameful thing, altars to make sacrificial smoke to Baal.”—Jer 11:13.

During exile and in apostolic period. During the period of the exile, the Jews who fled to Elephantine in Upper Egypt set up a temple and an altar, according to the Elephantine Papyri; and some centuries later the Jews near Leontopolis did likewise. (Jewish Antiquities, XIII, 62-68 [iii, 1]; The Jewish War, VII, 420-432 [x, 2, 3]) This latter temple and altar were built by Priest Onias in an attempt to fulfill Isaiah 19:19, 20.

In the Common Era, the apostle Paul in speaking to the Athenians referred to an altar inscribed “To an Unknown God.” (Ac 17:23) Ample historical information is available to corroborate this. Apollonius of Tyana, who visited Athens sometime after Paul, is reported to have said: “It is a much greater proof of wisdom and sobriety to speak well of all the gods, especially at Athens, where altars are set up in honour even of unknown gods.” (Philostratus, The Life of Apollonius of Tyana, VI, III) Geographer Pausanias in the second century C.E. reported that on the road from the Phaleron Bay harbor to the city of Athens he had observed “altars of the gods named Unknown, and of heroes.” He also spoke of “an altar of Unknown Gods” at Olympia. (Description of Greece, Attica, I, 4; Elis I, XIV, 8) A similar altar was discovered in 1909 at Pergamum in the precincts of the temple of Demeter.

Significance of Altars. In Hebrews chapters 8 and 9 the apostle Paul clearly shows that all the things related to the tabernacle and temple service were typical. (Heb 8:5; 9:23) The significance of the two altars is made evident by information in the Christian Greek Scriptures. The altar of burnt offerings represented God’s “will,” that is, his willingness to accept the perfect human sacrifice of his only-begotten Son. (Heb 10:5-10) Its location in front of the entrance to the sanctuary emphasizes the requirement of faith in that ransom sacrifice as a prerequisite for acceptance by God. (Joh 3:16-18) The insistence upon a single altar of sacrifice is in harmony with Christ’s declaration: “I am the way and the truth and the life. No one comes to the Father except through me,” as well as with the many texts declaring the unity to be manifest in the Christian faith.—Joh 14:6; Mt 7:13, 14; 1Co 1:10-13; Eph 4:3-6; note also Isaiah’s prophecy, at Isa 56:7; 60:7, that people of all nations would come to God’s altar.

It is notable that, though some individuals fled to the altar, taking hold of its horns, in hope of gaining protection, God’s law prescribed that the willful murderer was to be taken “even from being at my altar to die.” (Ex 21:14; compare 1Ki 1:50-53; 2:28-34.) The psalmist sang: “I shall wash my hands in innocency itself, and I will march around your altar, O Jehovah.”—Ps 26:6.

Although Hebrews 13:10 has been used as basis for erection of literal altars by professed Christians, the context shows that the “altar” spoken of by Paul is not literal but symbolic. (Heb 13:10-16) M’Clintock and Strong’s Cyclopædia (1882, Vol. I, p. 183) says concerning the early Christians: “When the ancient apologists were reproached with having no temples, no altars, no shrines, they simply replied, ‘Shrines and altars we have not.’” Commenting on Hebrews 13:10, M. R. Vincent’s Word Studies in the New Testament (1957, Vol. IV, p. 567) says: “It is a mistake to try to find in the Christian economy some specific object answering to altar—either the cross, or the eucharistic table, or Christ himself. Rather the ideas of approach to God,—sacrifice, atonement, pardon and acceptance, salvation,—are gathered up and generally represented in the figure of an altar, even as the Jewish altar was the point at which all these ideas converged.” The multiplying of altars was strongly condemned by the Hebrew prophets. (Isa 17:7, 8) Hosea said that Ephraim “multiplied altars in order to sin” (Ho 8:11; 10:1, 2, 8; 12:11); Jeremiah stated that the sin of Judah was engraved “on the horns of their altars” (Jer 17:1, 2); and Ezekiel foretold the slaughter of false worshipers “all around their altars” (Eze 6:4-6, 13).

Expressions of divine judgment are also prophetically associated with the true altar. (Isa 6:5-12; Eze 9:2; Am 9:1) It is from “underneath the altar” that the souls of those slaughtered for witnessing for God symbolically cry out: “Until when, Sovereign Lord holy and true, are you refraining from judging and avenging our blood upon those who dwell on the earth?”—Re 6:9, 10; compare 8:5; 11:1; 16:7.

At Revelation 8:3, 4 the golden altar of incense is expressly related to the prayers of the righteous. It was customary among the Jews to pray at “the hour of offering incense.” (Lu 1:9, 10; compare Ps 141:2.) The single altar for offering incense also corresponds with the one avenue of approach outlined in the Christian Greek Scriptures.—Joh 10:9; 14:6; 16:23; Eph 2:18-22; 

On Thomas emlyn and the one God:The Watchtower society's commentary.

Thomas Emlyn—Blasphemer or Advocate of Truth?


WHO was Thomas Emlyn, and what moved him to take a stand for truth? What might we learn from him that could help us today?

To answer those questions, we need to go back to the late 17th and early 18th centuries in England and Ireland. The Church of England then wielded considerable authority. Various Protestant groups and individuals were at odds with the church.

WHO WAS HE?

It was into this environment that Thomas Emlyn was born on May 27, 1663, at Stamford, Lincolnshire, England. At the age of 19, he preached his first sermon. Later, he became a chaplain for a countess who lived in London; and still later, he moved to Belfast, Ireland.


In Belfast he eventually officiated in a parish church. As time passed, Emlyn served as a minister in several places, including Dublin.

WHY WAS HE ACCUSED OF BLASPHEMY?

During those times, Emlyn was carefully studying the Bible. His studies caused him to doubt the Trinity, although he had originally believed in it. As he researched the Gospels, he became convinced that they supported his improved understanding.

Emlyn did not immediately reveal what he had found. However, some in his Dublin church noticed that he did not refer to the Trinity in his sermons. Knowing that his findings would not be received well by others, he wrote: “I cannot hope to continue here in my present post, when once I have professed.” In June 1702, two associates confronted him about the omission of the Trinity from his sermons. Emlyn confessed that he no longer believed in it and offered to resign.

Within a few days, he left Dublin, Ireland, for England. However, after ten weeks he returned to Dublin to settle some affairs, with the goal of moving to London permanently. While there, hoping to vindicate his views, he published An Humble Inquiry Into the Scripture-Account of Jesus Christ. In this publication, he gave clear Scriptural proof as to why Jesus could not be the Supreme God. This infuriated members of Emlyn’s former congregation in Dublin. A formal complaint was filed.

Emlyn was arrested and brought before the Queen’s Bench Court in Dublin on June 14, 1703. In his True Narrative of the Proceedings, Emlyn states that he was indicted “for writing and publishing a book, wherein, it says, I had blasphemously and maliciously asserted, etc. That Jesus Christ was not equal to God the Father.” The trial proved to be a farce. Seven bishops of the Church of Ireland sat on the bench with the judges. Emlyn was not allowed to speak in his  own defense. Richard Levins, a distinguished lawyer, told Emlyn that he would be run down “like a wolf, without law or game.” At the conclusion of the trial, Richard Pyne, Ireland’s Lord Chief Justice, told the jury that if they did not come to the expected verdict, his “lords the bishops were there,” perhaps implying that the jury would be duly punished.

When Emlyn was found guilty, the solicitor-general proposed that he retract. Emlyn refused. He was fined and sentenced to a year’s imprisonment. Because he could not pay the fine, he stayed in prison for two years until a friend convinced authorities to reduce the amount. Emlyn was released on July 21, 1705. The ignominies he suffered moved him to declare, as earlier quoted: “I suffer for what I take to be his [God’s] truth and glory.”


Emlyn moved to London, where he eventually associated with William Whiston, another Bible scholar who had been ostracized because he published what he felt was Bible truth. Whiston respected Emlyn, calling him “‘the first and principal confessor’ of ‘old christianity.’” 

WHY DID HE REJECT THE TRINITY?

Like William Whiston and another respected scholar, Isaac Newton, Emlyn found that the Bible does not support the Trinity doctrine as reflected in the Athanasian Creed. He explained: “After much serious thought, and study of the holy Scriptures, . . . I found great reason . . . to alter my judgment, in relation to formerly received opinions of the Trinity.” He concluded that “the God and Father of Jesus Christ is alone the Supreme Being.”

What brought Emlyn to that conclusion? He found many scriptures pointing to differences between Jesus and His Father. Here are just a few examples (Emlyn’s comments on the scriptures are in italics):

John 17:3: “Christ is never said to be that one God or so God, as to be the only God.” Only the Father is called “the only true God.”
John 5:30: “The Son does not his own will, but the will of the Father.”
John 5:26: “His Life is given him of the Father.”
Ephesians 1:3: “Whereas Jesus Christ is commonly styled the Son of God, we never find the Father styled the Father of God, tho he be oft called the Father of our Lord Jesus.”

After Emlyn considered all the evidence, he emphatically stated: “There is no one passage in holy Scripture, wherein it can be so much as pretended, that the Father, Son, and Holy Spirit are expressly said to be one and the same individual being.”

WHAT CAN WE LEARN?

Many today back off from taking a stand for what the Scriptures teach. But Emlyn was willing to stand up for Bible truth. He raised the question, “If a man may not profess the most important truths, which he finds clear and evident in the holy Scriptures, to what end should he read and search them?” Emlyn would not compromise the truth.


The example set by Emlyn and others can move us to consider whether we are willing to stand up for the truth in the face of scorn. We too can ask ourselves, ‘Which is more important—the honor and blessing of the community or upholding the truth of God’s Word?’

On the laws of logic

Laws of thought  
Logic
Written by: The Editors of Encyclopædia Britannica

Laws of thought, traditionally, the three fundamental laws of logic: (1) the law of contradiction, (2) the law of excluded middle (or third), and (3) the principle of identity. That is, (1) for all propositions p, it is impossible for both p and not p to be true, or symbolically, ∼(p · ∼p), in which ∼ means “not” and · means “and”; (2) either p or ∼p must be true, there being no third or middle true proposition between them, or symbolically p ∨ ∼p, in which ∨ means “or”; and (3) if a propositional function F is true of an individual variable x, then F is indeed true of x, or symbolically F(x) ⊃ F(x), in which ⊃ means “formally implies.” Another formulation of the principle of identity asserts that a thing is identical with itself, or (∀x) (x = x), in which ∀ means “for every”; or simply that x is x.

Aristotle cited the laws of contradiction and of excluded middle as examples of axioms. He partly exempted future contingents, or statements about unsure future events, from the law of excluded middle, holding that it is not (now) either true or false that there will be a naval battle tomorrow, but that the complex proposition that either there will be a naval battle tomorrow or that there will not is (now) true. In the epochal Principia Mathematica (1910–13) of A.N. Whitehead and Bertrand Russell, this law occurs as a theorem rather than as an axiom.

That the laws of thought are a sufficient foundation for the whole of logic, or that all other principles of logic are mere elaborations of them, was a doctrine common among traditional logicians. It has been shown, however, that these laws do not even comprise a sufficient set of axioms for the most elementary branch of logic, the propositional calculus, nor for the traditional theory of the categorical syllogism or the logic of terms.

The law of excluded middle and certain related laws have been rejected by L.E.J. Brouwer, a Dutch mathematical intuitionist, and his school, who do not admit their use in mathematical proofs in which all members of an infinite class are involved. Brouwer would not accept, for example, the disjunction that either there occur ten successive 7’s somewhere in the decimal expansion of π or else not, since no proof is known of either alternative; but he would accept it if applied, for instance, to the first 10100 digits of the decimal, since these could in principle actually be computed.

In 1920 Jan Łukasiewicz, a leading member of the Polish school of logic, formulated a propositional calculus that had a third truth-value, neither truth nor falsity, for Aristotle’s future contingents, a calculus in which the laws of contradiction and of excluded middle both failed. Other systems have gone beyond three-valued to many-valued logics—e.g., certain probability logics having various degrees of truth-value between truth and falsity.

Of course only an academic could deny the axiomatic nature of the premise that a claim cannot be both true and false at the same time and/or in the same way or not realise that the fact that there are claims that are neither true nor false does not in anyway falsify that premise.